INFERNAL1/a [1.1 | October 2013] NAME AUF1_binding DESC AUF1 binding site STATES 103 NODES 27 CLEN 33 W 83 ALPH RNA RF no CONS yes MAP yes DATE Fri May 30 14:13:22 2014 COM [1] /share/data/bin/cmbuild -F /share/data/people/ppg15/motifs/AUF1_binding/CM /share/data/people/ppg15/motifs/AUF1_binding/SEED COM [2] /share/data/bin/cmcalibrate --mpi --seed 1 /share/data/people/ppg15/motifs/AUF1_binding/CM PBEGIN 0.05 PEND 0.05 WBETA 1e-07 QDBBETA1 1e-07 QDBBETA2 1e-15 N2OMEGA 1.52588e-05 N3OMEGA 1.52588e-05 ELSELF -0.08926734 NSEQ 8 EFFN 8.000000 CKSUM 3672993111 NULL 0.000 0.000 0.000 0.000 GA 16.00 EFP7GF -0.5364 0.86386 ECMLC 0.54192 -1.70246 8.47878 1600000 298791 0.004016 ECMGC 0.59034 0.82868 10.64859 1600000 131735 0.003036 ECMLI 0.60594 0.51114 9.27741 1600000 243265 0.004933 ECMGI 0.62046 2.10321 10.95213 1600000 96941 0.004126 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 83 145 -8.394 -8.601 -0.019 -7.015 IL 1 1 2 1 4 1 8 85 147 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 7 85 146 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 1 ] 1 - U - - - ML 3 2 3 5 5 1 9 83 145 -8.355 -0.016 -8.170 -8.382 -9.274 -0.696 -1.802 -1.016 1.379 D 4 2 3 5 5 0 2 81 143 -4.959 -0.803 -4.221 -2.596 -2.508 IL 5 5 3 5 5 1 6 83 145 -2.408 -0.496 -4.087 -5.920 -5.193 0.000 0.000 0.000 0.000 [ MATP 2 ] 2 39 g u - - MP 6 5 3 10 6 2 9 82 144 -9.837 -9.776 -0.013 -8.553 -8.832 -9.227 -4.713 -4.508 -4.627 -0.818 -3.694 -5.290 0.633 -4.329 -4.608 -0.682 -5.025 2.245 1.855 -4.938 2.148 -3.510 ML 7 5 3 10 6 1 4 80 142 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 8 5 3 10 6 1 3 80 142 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 9 5 3 10 6 0 1 78 139 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 10 10 5 10 6 1 5 81 143 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 11 11 6 11 5 1 5 81 143 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 3 ] 3 38 A U - - MP 12 11 6 16 4 2 7 80 142 -8.394 -8.601 -0.019 -7.015 -4.499 -3.637 -4.618 3.057 -4.937 -6.009 -0.683 -4.710 -4.457 0.114 -5.034 0.949 1.778 -5.111 -2.616 -3.440 ML 13 11 6 16 4 1 3 79 141 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 14 11 6 16 4 1 2 78 140 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 15 11 6 16 4 0 1 77 139 -4.568 -4.250 -2.265 -0.520 IL 16 16 5 16 4 1 4 80 142 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 17 17 6 17 3 1 4 80 141 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 4 ] 4 - U - - - ML 18 17 6 20 3 1 5 78 140 -9.343 -0.008 -7.997 -2.223 0.483 -3.098 1.184 D 19 17 6 20 3 0 1 76 138 -6.174 -1.687 -0.566 IL 20 20 3 20 3 1 3 79 140 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 5 ] 5 - a - - - ML 21 20 3 23 3 1 5 77 139 -9.674 -0.007 -7.992 0.615 -1.489 -0.100 0.238 D 22 20 3 23 3 0 0 75 137 -5.620 -0.734 -1.403 IL 23 23 3 23 3 1 3 77 139 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 6 ] - 37 - a - - MR 24 23 3 26 3 1 4 76 138 -9.674 -0.007 -7.992 0.359 -0.253 0.065 -0.264 D 25 23 3 26 3 0 0 74 136 -6.390 -1.568 -0.620 IR 26 26 3 26 3 1 2 76 138 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 7 ] - 36 - a - - MR 27 26 3 29 3 1 4 75 137 -9.674 -0.007 -7.992 0.433 -0.367 -0.209 0.014 D 28 26 3 29 3 0 0 73 135 -6.390 -1.568 -0.620 IR 29 29 3 29 3 1 2 75 137 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 8 ] - 35 - U - - MR 30 29 3 32 5 1 3 74 136 -8.355 -0.016 -8.170 -8.382 -9.274 -0.089 -2.034 -2.465 1.397 D 31 29 3 32 5 0 0 72 134 -5.352 -0.707 -2.978 -4.409 -2.404 IR 32 32 3 32 5 1 2 74 136 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 9 ] 6 34 u a - - MP 33 32 3 37 4 2 3 73 135 -8.394 -8.601 -0.019 -7.015 -3.996 -3.784 -4.023 0.036 -3.233 -4.799 1.802 -3.819 -3.998 2.058 -4.490 -1.620 2.267 -4.183 0.558 -2.846 ML 34 32 3 37 4 1 1 72 134 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 35 32 3 37 4 1 1 71 133 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 36 32 3 37 4 0 0 70 132 -4.568 -4.250 -2.265 -0.520 IL 37 37 5 37 4 1 1 73 135 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 38 38 6 38 3 1 1 73 134 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 10 ] 7 - A - - - ML 39 38 6 41 5 1 2 71 133 -8.355 -0.016 -8.170 -8.382 -9.274 1.428 -2.192 -2.335 -0.165 D 40 38 6 41 5 0 0 69 131 -4.959 -0.803 -4.221 -2.596 -2.508 IL 41 41 3 41 5 1 1 71 133 -2.408 -0.496 -4.087 -5.920 -5.193 0.000 0.000 0.000 0.000 [ MATP 11 ] 8 33 c g - - MP 42 41 3 46 4 2 2 70 132 -8.394 -8.601 -0.019 -7.015 -3.083 -3.060 -3.217 1.447 -2.816 -4.040 1.711 -3.290 -3.228 0.579 -3.764 1.393 1.477 -3.360 0.970 -2.252 ML 43 41 3 46 4 1 1 69 131 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 44 41 3 46 4 1 1 68 130 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 45 41 3 46 4 0 0 67 129 -4.568 -4.250 -2.265 -0.520 IL 46 46 5 46 4 1 1 70 132 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 47 47 6 47 3 1 1 70 131 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 12 ] 9 - a - - - ML 48 47 6 50 3 1 1 68 130 -9.343 -0.150 -3.364 0.850 -0.733 -0.229 -0.431 D 49 47 6 50 3 0 0 66 128 -6.174 -1.687 -0.566 IL 50 50 3 50 3 1 1 69 130 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 13 ] 10 - c - - - ML 51 50 3 53 3 1 1 67 129 -9.202 -0.009 -7.856 -1.154 0.883 -0.292 -0.169 D 52 50 3 53 3 0 0 66 128 -7.871 -0.345 -2.263 IL 53 53 3 53 3 1 1 68 129 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 14 ] 11 - U - - - ML 54 53 3 56 5 1 1 66 128 -8.355 -0.016 -8.170 -8.382 -9.274 -0.152 -0.893 -2.034 1.212 D 55 53 3 56 5 0 0 64 126 -4.959 -0.803 -4.221 -2.596 -2.508 IL 56 56 3 56 5 1 1 66 128 -2.408 -0.496 -4.087 -5.920 -5.193 0.000 0.000 0.000 0.000 [ MATP 15 ] 12 32 a u - - MP 57 56 3 61 6 2 2 65 127 -9.837 -9.776 -0.013 -8.553 -8.832 -9.227 -3.528 -3.253 -3.623 2.723 -3.365 -4.476 1.341 -3.738 -3.653 0.697 -4.171 0.588 0.371 -3.787 0.667 -2.636 ML 58 56 3 61 6 1 1 64 125 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 59 56 3 61 6 1 1 63 125 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 60 56 3 61 6 0 0 61 123 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 61 61 5 61 6 1 1 64 126 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 62 62 6 62 5 1 1 64 126 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 16 ] 13 31 a u - - MP 63 62 6 67 4 2 2 63 125 -8.394 -8.601 -0.019 -7.015 -3.046 -2.993 -3.177 2.009 -2.842 -3.999 1.683 -3.291 -3.207 0.732 -3.741 1.144 1.292 -3.311 0.361 -2.231 ML 64 62 6 67 4 1 1 62 124 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 65 62 6 67 4 1 1 62 123 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 66 62 6 67 4 0 0 60 122 -4.568 -4.250 -2.265 -0.520 IL 67 67 5 67 4 1 1 63 125 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 68 68 6 68 3 1 1 63 124 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 17 ] 14 - a - - - ML 69 68 6 71 3 1 1 61 123 -9.674 -0.007 -7.992 0.625 0.436 -1.883 -0.262 D 70 68 6 71 3 0 0 60 121 -5.620 -0.734 -1.403 IL 71 71 3 71 3 1 1 61 123 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 18 ] - 30 - c - - MR 72 71 3 74 3 1 1 60 122 -9.674 -0.007 -7.992 -0.225 0.232 -0.049 0.005 D 73 71 3 74 3 0 0 58 120 -6.390 -1.568 -0.620 IR 74 74 3 74 3 1 1 60 122 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 19 ] - 29 - a - - MR 75 74 3 77 5 1 1 59 121 -8.355 -0.016 -8.170 -8.382 -9.274 0.616 0.267 -1.782 -0.040 D 76 74 3 77 5 0 0 57 119 -5.352 -0.707 -2.978 -4.409 -2.404 IR 77 77 3 77 5 1 1 59 121 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 20 ] 15 28 a u - - MP 78 77 3 82 6 2 2 58 120 -9.837 -9.776 -0.013 -8.553 -8.832 -9.227 -4.352 -4.202 -4.324 2.698 -3.436 -5.030 2.038 -4.065 -4.305 -0.198 -4.760 -2.090 1.701 -4.552 -1.090 -3.184 ML 79 77 3 82 6 1 1 56 118 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 80 77 3 82 6 1 1 56 117 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 81 77 3 82 6 0 0 53 115 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 82 82 5 82 6 1 1 57 119 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 83 83 6 83 5 1 1 57 119 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 21 ] 16 27 u a - - MP 84 83 6 88 4 2 2 56 118 -8.394 -8.601 -0.019 -7.015 -2.958 -2.936 -3.093 1.390 -2.771 -3.928 1.644 -3.219 -3.127 1.366 -3.669 0.384 1.893 -3.227 0.524 -2.156 ML 85 83 6 88 4 1 1 55 117 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 86 83 6 88 4 1 1 54 115 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 87 83 6 88 4 0 0 52 114 -4.568 -4.250 -2.265 -0.520 IL 88 88 5 88 4 1 1 56 118 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 89 89 6 89 3 1 1 56 117 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 22 ] 17 - A - - - ML 90 89 6 92 3 1 1 54 116 -9.343 -0.008 -7.997 1.102 -0.763 -0.934 -0.434 D 91 89 6 92 3 0 0 50 111 -6.174 -1.687 -0.566 IL 92 92 3 92 3 1 1 55 116 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 23 ] 18 - A - - - ML 93 92 3 95 3 1 1 53 115 -1.870 -0.629 -3.651 1.599 -3.267 -0.435 -2.967 D 94 92 3 95 3 0 0 42 104 -6.174 -1.687 -0.566 IL 95 95 3 95 3 1 1 56 118 -0.430 -1.991 -7.282 0.000 0.000 0.000 0.000 [ MATL 24 ] 25 - A - - - ML 96 95 3 98 3 1 1 12 31 -9.230 -0.009 -7.884 1.044 -0.203 -0.705 -1.131 D 97 95 3 98 3 0 0 12 31 -7.670 -0.404 -2.062 IL 98 98 3 98 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 25 ] 26 - a - - - ML 99 98 3 101 2 1 1 1 1 * 0.000 0.944 -0.879 0.195 -1.368 D 100 98 3 101 2 0 0 0 0 * 0.000 IL 101 101 3 101 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 26 ] - - - - - - E 102 101 3 -1 0 0 0 0 0 // HMMER3/f [i1.1 | October 2013] NAME AUF1_binding DESC AUF1 binding site LENG 33 MAXL 106 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Fri May 30 14:13:22 2014 COM [1] /share/data/bin/cmbuild -F /share/data/people/ppg15/motifs/AUF1_binding/CM /share/data/people/ppg15/motifs/AUF1_binding/SEED NSEQ 8 EFFN 7.652344 CKSUM 3672993111 STATS LOCAL MSV -9.0397 0.86386 STATS LOCAL VITERBI -10.5506 0.86386 STATS LOCAL FORWARD -1.5091 0.86386 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.20225 1.72069 1.57578 1.15933 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 0.00000 * 1 1.85709 2.60471 2.08585 0.43735 1 U - - : 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 2 3.03735 2.18275 1.09110 0.68625 2 U - - < 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 3 0.65120 3.00709 1.62506 1.45997 3 A - - < 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 4 2.87919 1.05631 3.48311 0.57027 4 U - - - 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 5 0.96339 2.39740 1.45769 1.22189 5 a - - - 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 6 2.52544 1.45771 1.25254 0.91272 6 u - - < 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 7 0.40307 2.86777 2.96395 1.49927 7 A - - - 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 8 1.64729 1.49281 1.31602 1.15681 8 u - - < 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 9 0.80127 1.89089 1.54586 1.67570 9 a - - - 1.38629 1.38629 1.38629 1.38629 0.11625 4.62497 2.30318 1.46634 0.26236 1.09861 0.40547 10 2.15684 0.78420 1.59129 1.49540 10 c - - - 1.38629 1.38629 1.38629 1.38629 0.02179 4.53051 4.53051 1.46634 0.26236 0.17915 1.80779 11 1.48903 1.99521 2.76782 0.55230 11 U - - - 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 12 0.86699 1.74540 1.57234 1.62125 12 a - - < 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 13 1.30250 1.51271 1.36952 1.37197 13 a - - < 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 14 0.95653 1.09126 2.66344 1.55934 14 a - - - 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 15 0.89651 1.31412 2.53165 1.41153 15 a - - < 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 16 1.67104 1.53012 1.36729 1.07693 16 u - - < 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 17 0.62796 1.91111 2.02717 1.67827 17 A - - _ 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 18 0.28211 3.59961 1.68983 3.38362 18 A - - _ 1.38629 1.38629 1.38629 1.38629 0.43981 1.29891 2.48878 1.55802 0.23642 1.09861 0.40547 19 0.66971 1.53082 1.87012 2.13979 25 A - - _ 1.38629 1.38629 1.38629 1.38629 0.02138 4.54895 4.54895 1.46634 0.26236 0.21205 1.65510 20 0.73753 1.99142 1.25588 2.29881 26 a - - _ 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 21 1.36298 1.70711 1.21200 1.32760 27 g - - > 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 22 1.53152 2.71053 1.22749 0.85740 28 u - - > 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 23 0.96275 1.20660 2.59595 1.40906 29 a - - - 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 24 1.53561 1.23093 1.42400 1.37869 30 c - - - 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 25 1.72413 2.07067 1.23049 0.90777 31 u - - > 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 26 2.27111 2.10896 1.32195 0.67565 32 U - - > 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 27 1.61691 2.16774 1.08758 1.04976 33 u - - > 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 28 1.16084 1.31486 1.14857 2.29087 34 g - - > 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 29 1.44669 2.75684 3.05180 0.42482 35 U - - - 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 30 1.08801 1.64071 1.53257 1.37322 36 a - - - 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 31 1.13818 1.56418 1.34498 1.56164 37 a - - - 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 32 1.50736 2.50977 2.81972 0.45005 38 U - - > 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 33 1.44229 2.99213 0.97503 1.08989 39 g - - > 1.38629 1.38629 1.38629 1.38629 0.00995 4.61512 * 1.46634 0.26236 0.00000 * //